Equivalence class NR_4.0_35054.5 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3IGI|1|A (rep) | Group IIC intron, 5'-R(*CP*GP*CP*UP*CP*UP*AP*CP*UP*CP*UP*AP*U)-3' | Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron | X-ray diffraction | 3.12 | 2009-12-22 | ||||
| 2 | 8OLV|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and ARN25850 | X-ray diffraction | 2.81 | 2024-06-19 |
| 3 | 5J02|1|A | Group II catalytic intron D1-D4-1 | GROUP II INTRON LARIAT, 5' EXON ANALOG (5'-R(*CP*UP*GP*UP*UP*AP*(5MU))-3') | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+, MG2+ and an inactive 5' exon. | X-ray diffraction | 3.49 | 2016-12-14 |
| 4 | 4FAX|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Na+ and Mg2+ | X-ray diffraction | 3.1 | 2012-11-14 |
| 5 | 4FAR|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exon | X-ray diffraction | 2.86 | 2012-11-14 |
| 6 | 8OLS|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and intronistat B | X-ray diffraction | 3 | 2024-06-19 |
| 7 | 4E8N|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of NH4+ and Mg2+ | X-ray diffraction | 2.96 | 2012-11-14 |
| 8 | 6T3S|1|A | Group II catalytic intron D1-D4-1 | Group IIC Intron Ribozyme | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of Na+, Mg2+ and 5'-exon | X-ray diffraction | 3.28 | 2020-05-13 |
| 9 | 8OLY|1|A | Group II catalytic intron D1-D4-3 | Group IIC intron, 5'-exon | Oceanobacillus iheyensis | Bacteria | RF02001 | Structure of Oceanobacillus iheyensis group II intron post first step of splicing in the presence of K+, Mg2+ and intronistat B | X-ray diffraction | 3.11 | 2024-06-19 |
| 10 | 8RUI|1|A | Group II catalytic intron D1-D4-3 | Domains 1-5 | Oceanobacillus iheyensis | Bacteria | RF02001 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and intronistat B after 1h soaking | X-ray diffraction | 3.31 | 2024-06-19 |
| 11 | 4FAU|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+ and 5'-exon | X-ray diffraction | 2.87 | 2012-11-14 |
| 12 | 4FB0|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron C377G mutant in a ligand-free state in the presence of K+ and Mg2+ | X-ray diffraction | 3.22 | 2012-11-14 |
| 13 | 8RUJ|1|A | Group II catalytic intron D1-D4-3 | Domains 1-5 | Oceanobacillus iheyensis | Bacteria | RF02001 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and ARN25850 after 1h soaking | X-ray diffraction | 3.12 | 2024-06-19 |
| 14 | 4E8K|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron, 5'-R(*CP*G*AP*UP*UP*UP*AP*UP*UP*A)-3' | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and a non-hydrolyzed oligonucleotide substrate | X-ray diffraction | 3.03 | 2012-11-14 |
| 15 | 4E8Q|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Tl+ and Mg2+ | X-ray diffraction | 2.84 | 2012-11-14 |
| 16 | 4Y1O|1|A | Group II catalytic intron D1-D4-3 | group II intron, domain 1 | Oceanobacillus iheyensis | Bacteria | RF02001 | Oceanobacillus iheyensis group II intron domain 1 | X-ray diffraction | 2.95 | 2015-10-14 |
| 17 | 4Y1O|1|B | Group II catalytic intron D1-D4-3 | group II intron, domain 1 | Oceanobacillus iheyensis | Bacteria | RF02001 | Oceanobacillus iheyensis group II intron domain 1 | X-ray diffraction | 2.95 | 2015-10-14 |
| 18 | 6T3N|1|A | Group II catalytic intron D1-D4-1 | Group IIC Intron Ribozyme | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of Na+, Mg2+ and 5'-exon | X-ray diffraction | 3.22 | 2020-05-13 |
| 19 | 4E8P|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Rb+ and Mg2+ | X-ray diffraction | 3.28 | 2012-11-14 |
| 20 | 4E8T|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron, 5'-R(*AP*UP*UP*UP*AP*UP*UP*A)-3' | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and an oligonucleotide fragment substrate (low energy dataset) | X-ray diffraction | 3.34 | 2012-11-14 |
| 21 | 5J01|1|A | Group II catalytic intron D1-D4-1 | group II intron lariat | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+ and MG2+. | X-ray diffraction | 3.39 | 2016-12-14 |
| 22 | 4FAW|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron, 5'-R(*A*UP*UP*UP*AP*UP*UP*A)-3' | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and a hydrolyzed oligonucleotide fragment | X-ray diffraction | 2.7 | 2012-11-14 |
| 23 | 3EOH|1|A | Group IIC intron, 5'-R(*UP*UP*AP*UP*UP*A)-3' | Refined group II intron structure | X-ray diffraction | 3.12 | 2008-10-28 | ||||
| 24 | 8RUM|1|A | Group II catalytic intron D1-D4-1 | Domains 1-5 | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and intronistat B | X-ray diffraction | 3.62 | 2024-06-19 |
| 25 | 8RUL|1|A | Group II catalytic intron D1-D4-1 | Domains 1-5 | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of Li+ and Mg2+ | X-ray diffraction | 3.62 | 2024-06-19 |
| 26 | 6T3R|1|A | Group II catalytic intron D1-D4-1 | Group IIC Intron Ribozyme | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of K+, Mg2+ and 5'-exon | X-ray diffraction | 3.57 | 2020-05-13 |
| 27 | 4FAQ|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and 5'-exon | X-ray diffraction | 3.11 | 2012-11-14 |
| 28 | 4E8R|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Cs+ and Mg2+ | X-ray diffraction | 3.36 | 2012-11-14 |
| 29 | 8OLZ|1|A | Group II catalytic intron D1-D4-3 | DOMAINS 1-5, 5'-exon | Oceanobacillus iheyensis | Bacteria | RF02001 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and intronistat B after 2h30 soaking | X-ray diffraction | 3.31 | 2024-06-19 |
| 30 | 8RUN|1|A | Group II catalytic intron D1-D4-1 | Domains 1-5 | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and ARN25850 | X-ray diffraction | 3.73 | 2024-06-19 |
| 31 | 8OLW|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron before the first step of splicing in the presence of K+, Ca2+ and intronistat B | X-ray diffraction | 4 | 2024-06-19 |
| 32 | 4Y1N|1|B | Group II catalytic intron D1-D4-3 | group II intron, domain 1 | Oceanobacillus iheyensis | Bacteria | RF02001 | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-ray diffraction | 3 | 2015-10-14 |
| 33 | 3G78|1|A | Group II catalytic intron D1-D4-1 | Group II intron, Ligated EXON product | Oceanobacillus iheyensis | Bacteria | RF01998 | Insight into group II intron catalysis from revised crystal structure | X-ray diffraction | 2.8 | 2010-02-16 |
| 34 | 4E8M|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+ | X-ray diffraction | 3.5 | 2012-11-14 |
| 35 | 6T3K|1|A | Group II catalytic intron D1-D4-1 | Group IIC Intron Ribozyme | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exon | X-ray diffraction | 3.44 | 2020-05-13 |
| 36 | 4Y1N|1|A | Group II catalytic intron D1-D4-3 | group II intron, domain 1 | Oceanobacillus iheyensis | Bacteria | RF02001 | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-ray diffraction | 3 | 2015-10-14 |
| 37 | 4DS6|1|A | Group II catalytic intron D1-D4-1 | Mutant Group IIC Intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Crystal structure of a group II intron in the pre-catalytic state | X-ray diffraction | 3.64 | 2012-04-18 |
| 38 | 3EOG|1|A | Group IIC intron, 5'-R(*UP*UP*AP*UP*UP*A)-3' | Co-crystallization showing exon recognition by a group II intron | X-ray diffraction | 3.39 | 2008-10-28 | ||||
| 39 | 8OM0|1|A | Group II catalytic intron D1-D4-1 | Domains 1-5 | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+ and intronistat B | X-ray diffraction | 3.61 | 2024-06-19 |
| 40 | 3BWP|1|A | Group IIC intron | Crystal structure of a self-spliced group II intron | X-ray diffraction | 3.1 | 2008-04-15 | ||||
| 41 | 4E8V|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Ba2+ | X-ray diffraction | 3.99 | 2012-11-14 |
Release history
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
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Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
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Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. Instances are ordered to put similar structures near each other. The colorbar ranges from 0 to the maximum observed discrepancy, up to 0.5
#S - ordering by similarity (same as in the heat map).| #S | PDB | Title | Method | Resolution | Length |
|---|---|---|---|---|---|
| 1 | 5J01|1|A | Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+ and MG2+. | X-RAY DIFFRACTION | 3.39 | 414 |
| 2 | 5J02|1|A | Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+, MG2+ and an inactive 5' exon. | X-RAY DIFFRACTION | 3.49 | 414 |
| 3 | 3EOG|1|A | Co-crystallization showing exon recognition by a group II intron | X-RAY DIFFRACTION | 3.39 | 388 |
| 4 | 3BWP|1|A | Crystal structure of a self-spliced group II intron | X-RAY DIFFRACTION | 3.1 | 356 |
| 5 | 3EOH|1|A | Refined group II intron structure | X-RAY DIFFRACTION | 3.12 | 381 |
| 6 | 4DS6|1|A | Crystal structure of a group II intron in the pre-catalytic state | X-RAY DIFFRACTION | 3.64 | 393 |
| 7 | 6T3N|1|A | Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of Na+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 3.22 | 394 |
| 8 | 6T3S|1|A | Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of Na+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 3.28 | 393 |
| 9 | 4FAX|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Na+ and Mg2+ | X-RAY DIFFRACTION | 3.1 | 392 |
| 10 | 8RUM|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and intronistat B | X-RAY DIFFRACTION | 3.62 | 393 |
| 11 | 8OM0|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+ and intronistat B | X-RAY DIFFRACTION | 3.61 | 390 |
| 12 | 8RUN|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and ARN25850 | X-RAY DIFFRACTION | 3.73 | 393 |
| 13 | 8RUL|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of Li+ and Mg2+ | X-RAY DIFFRACTION | 3.62 | 394 |
| 14 | 4E8R|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Cs+ and Mg2+ | X-RAY DIFFRACTION | 3.36 | 393 |
| 15 | 4E8N|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of NH4+ and Mg2+ | X-RAY DIFFRACTION | 2.96 | 393 |
| 16 | 4E8Q|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Tl+ and Mg2+ | X-RAY DIFFRACTION | 2.84 | 393 |
| 17 | 4E8P|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Rb+ and Mg2+ | X-RAY DIFFRACTION | 3.28 | 393 |
| 18 | 4FB0|1|A | Structure of Oceanobacillus iheyensis group II intron C377G mutant in a ligand-free state in the presence of K+ and Mg2+ | X-RAY DIFFRACTION | 3.22 | 393 |
| 19 | 8OLS|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and intronistat B | X-RAY DIFFRACTION | 3 | 390 |
| 20 | 8OLV|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and ARN25850 | X-RAY DIFFRACTION | 2.81 | 394 |
| 21 | 8RUI|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and intronistat B after 1h soaking | X-RAY DIFFRACTION | 3.31 | 390 |
| 22 | 8RUJ|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and ARN25850 after 1h soaking | X-RAY DIFFRACTION | 3.12 | 390 |
| 23 | 4E8M|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+ | X-RAY DIFFRACTION | 3.5 | 394 |
| 24 | 4FAW|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and a hydrolyzed oligonucleotide fragment | X-RAY DIFFRACTION | 2.7 | 390 |
| 25 | 4FAU|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 2.87 | 395 |
| 26 | 4FAR|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 2.86 | 390 |
| 27 | 6T3K|1|A | Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 3.44 | 390 |
| 28 | 8OLY|1|A | Structure of Oceanobacillus iheyensis group II intron post first step of splicing in the presence of K+, Mg2+ and intronistat B | X-RAY DIFFRACTION | 3.11 | 390 |
| 29 | 6T3R|1|A | Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of K+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 3.57 | 389 |
| 30 | 8OLZ|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and intronistat B after 2h30 soaking | X-RAY DIFFRACTION | 3.31 | 390 |
| 31 | 3IGI|1|A | Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron | X-RAY DIFFRACTION | 3.12 | 389 |
| 32 | 3G78|1|A | Insight into group II intron catalysis from revised crystal structure | X-RAY DIFFRACTION | 2.8 | 389 |
| 33 | 4E8T|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and an oligonucleotide fragment substrate (low energy dataset) | X-RAY DIFFRACTION | 3.34 | 388 |
| 34 | 4E8K|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and a non-hydrolyzed oligonucleotide substrate | X-RAY DIFFRACTION | 3.03 | 388 |
| 35 | 4FAQ|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and 5'-exon | X-RAY DIFFRACTION | 3.11 | 396 |
| 36 | 8OLW|1|A | Structure of Oceanobacillus iheyensis group II intron before the first step of splicing in the presence of K+, Ca2+ and intronistat B | X-RAY DIFFRACTION | 4 | 396 |
| 37 | 4E8V|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Ba2+ | X-RAY DIFFRACTION | 3.99 | 389 |
| 38 | 4Y1O|1|B | Oceanobacillus iheyensis group II intron domain 1 | X-RAY DIFFRACTION | 2.95 | 256 |
| 39 | 4Y1N|1|A | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-RAY DIFFRACTION | 3 | 249 |
| 40 | 4Y1O|1|A | Oceanobacillus iheyensis group II intron domain 1 | X-RAY DIFFRACTION | 2.95 | 258 |
| 41 | 4Y1N|1|B | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-RAY DIFFRACTION | 3 | 259 |
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